To speed up the implementation of the two-dimensional materials in the development of potential biomedical applications, the toxicological aspects toward human health need to be addressed. Due to time-consuming and expensive analysis, only part of the continuously expanding family of 2D materials can be tested in vitro. The machine learning methods can be used—by extracting new insights from available biological data sets, and provide further guidance for experimental studies. This study identifies the most relevant highly surface-specific features that might be responsible for cytotoxic behavior of 2D materials, especially MXenes. In particular, two factors, namely, the presence of transition metal oxides and lithium atoms on the surface, are identified as cytotoxicity-generating features. The developed machine learning model succeeds in predicting toxicity for other 2D MXenes, previously not tested in vitro, and hence, is able to complement the existing knowledge coming from in vitro studies. Thus, we claim that it might be one of the solutions for reducing the number of toxicological studies needed, and allows for minimizing failures in future biological applications.